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Base Stacking (base + stacking)
Selected AbstractsOligonucleotide Analogues with Integrated Bases and Backbone.HELVETICA CHIMICA ACTA, Issue 12 2006Abstract The self-complementary UA and AU dinucleotide analogues 41,45, 47, 48, and 51,60 were prepared by Sonogashira coupling of 6-iodouridines with C(5,) -ethynylated adenosines and of 8-iodoadenosines with C(5,) -ethynylated uridines. The dinucleotide analogues associate in CDCl3 solution. The C(6/I) -unsubstituted AU dimers 51 and 54 prefer an anti -oriented uracilyl group and form stretched linear duplexes. The UA propargyl alcohols 41 and 43,45 possess a persistent intramolecular O(5,/I)H,,,N(3/I) H-bond and, thus, a syn -oriented adeninyl and a gt - or tg -oriented ethynyl moiety; they form corrugated linear duplexes. All other dimers form cyclic duplexes characterized by syn -oriented nucleobases. The preferred orientation of the ethynyl moiety (the C(4,),C(5,) torsion angle) defines a conformation between gg and one where the ethynyl group eclipses O(4,/I). The UA dimers 42, 47, and 48 form Watson,Crick H-bonds, the AU dimers 56 and 58,60 H-bonds of the Watson,Crick -type, the AU dimers 53 and 55 reverse- Hoogsteen, and 57Hoogsteen H-bonds. The pairing mode depends on the substituent of C(5,/I) (H, OSiiPr3; OH) and on the H-bonds of HOC(5,/I) in the AU dimers. Association constants were derived from the concentration-dependent chemical shift for HN(3) of the uracilyl moiety; they vary from 45,104,M,1 for linear duplexes to 197,2307,M,1 for cyclic duplexes. The thermodynamic parameters were determined by van't Hoff analysis of the temperature-dependence of the (concentration-dependent) chemical shift for HN(3) of the uracilyl moiety. Neglecting stacking energies, one finds an average energy of 3.5,4.0,kcal/mol per intermolecular H-bond. Base stacking is evidenced by the temperature-dependent CD spectra. The crystal structure of 54 shows two antiparallel chains of dimers connected by Watson-Crick H-bonds. The chains are bridged by a strong H-bond between the propargylic OH and OC(4) and by weak reverse A,,,A Hoogsteen H-bonds. [source] Enhanced pH-mediated stacking of anions for CE incorporating a dynamic pH junctionELECTROPHORESIS, Issue 20 2007Stacy D. Arnett Abstract A technique has been developed to enhance analyte focusing for CE for the analysis of physiological samples. High-ionic-strength samples are titrated to low-ionic-strength on-line using pH-mediated sample stacking in conjunction with a dynamic pH junction. This method concentrates analytes by reducing their electrophoretic mobility during field-amplification. Parameters responsible for enhanced focusing were investigated, and an enhanced pH-mediated stacking method was optimized for anionic nucleosides. The process results in ultra-narrow peak widths, for example, 0.28,s for thymidine with a 10,min analysis time. Peak width and resolution with the enhanced stacking method were also compared to normal base stacking and electrokinetic injection. With this technique, mass-loading capacity can be increased without degradation in peak shape and resolution is dramatically improved. [source] Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stackingJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2003Stephen C. Harvey Abstract In building and refining nucleic acid structures, it is often desirable to enforce particular base pairing and/or base stacking interactions. Energy-based modeling programs with classical molecular mechanics force fields do not lend themselves to the easy imposition of penalty terms corresponding to such restraints, because the requirement that two bases lie in or near the same plane (pairing) or that they lie in parallel planes (stacking) cannot be easily expressed in terms of traditional interactions involving two atoms (bonds), three atoms (angles), or four atoms (torsions). Here we derive expressions that define a collection of pseudobonds and pseudoangles through which molecular mechanics restraints for base pairing and stacking can be imposed. We have implemented these restraints into the JUMNA package for modeling DNA and RNA structures. JUMNA scripts can specify base pairing with a variety of standard geometries (Watson,Crick, Hoogsteen, wobble, etc.), or with user-defined geometries; they can also specify stacking arrangements. We have also implemented "soft-core" functions to modify van der Waals and electrostatic interactions to avoid steric conflicts in particularly difficult refinements where two backbones need to pass through one another. Test cases are presented to show the utility of the method. The restraints could be adapted for implementation in other molecular mechanics packages. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 1,9, 2003 [source] Studies of the intermolecular DNA triplexes of C+·GC and T·AT triplets by electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 2 2008Cuihong Wan Abstract Formation and stabilities of four 14-mer intermolecular DNA triplexes, consisting of third strands with repeating sequence CTCT, CCTT, CTT, or TTT, were studied by electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in the gas phase. The gas-phase stabilities of the triplexes were compared with their CD spectra and melting behaviors in solution, and parallel correlation between two phases were obtained. In the presence of 20 mM NH4+ (pH 5.5), the formation of the TTT triplex was not detected in both solution and the gas phase. Other triplexes showed the same order, CTCT > CCTT > CTT, of ion abundances in mass spectra and Tm values in solution. The more stable triplexes are those that contained higher percentage of C+·GC triplets and an alternating CT sequence. However, the CCTT with the same C+·GC triplets as the CTCT showed a higher stability than the latter during the gas-phase dissociation. Furthermore, a biphasic triplex-to-duplex-to-single transition was detected in the gas phase, while a monophasic triplex-to-single dissociation was observed in solution. The present results reveal that hydrogen bonds and electrostatic interactions dominate in the gas phase, while base stacking and hydrophobic interactions dominate in solution to stabilize the triplexes. Moreover, weak acidic conditions (pH 5,6) promote the formation of the parallel triplexes. Copyright © 2007 John Wiley & Sons, Ltd. [source] Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopyBIOPOLYMERS, Issue 1 2006Lydie Grajcar Abstract We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag] sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl, and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA > pdA and (pA)n , (pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6,28, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||